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Abstract
Among its attributes, the mythical philosopher’s stone is supposedly capable of turning base metals to gold or silver. In an analogous fashion, we are finding that protein crystallization optimization using ionic liquids (ILs) often results in the conversion of base protein precipitate to crystals. Recombinant inorganic pyrophosphatases (8 of the 11 proteins) from pathogenic bacteria as well as several other proteins were tested for optimization by 23 ILs, plus a dH2O control, at IL concentrations of 0.1, 0.2, and 0.4 M. The ILs were used as additives, and all proteins were crystallized in the presence of at least one IL. For 9 of the 11 proteins, precipitation conditions were converted to crystals with at least one IL. The ILs could be ranked in order of effectiveness, and it was found that ~83% of the precipitation-derived crystallization conditions could be obtained with a suite of just eight ILs, with the top two ILs accounting for ~50% of the hits. Structural trends were found in the effectiveness of the ILs, with shorter-alkyl-chain ILs being more effective. The two top ILs, accounting for ~50% of the unique crystallization results, were choline dihydrogen phosphate and 1-butyl-3-methylimidazolium tetrafluoroborate. Curiously, however, a butyl group was present on the cation of four of the top eight ILs.
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Affiliation(s)
- Crissy L. Tarver
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Qunying Yuan
- Department of Biological and Environmental Science, Alabama A&M University, Normal, AL 35762, USA
| | - Marc L. Pusey
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35805, USA
- Correspondence: ; Tel.: +1-256-701-7214
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Anashkin VA, Aksenova VA, Salminen A, Lahti R, Baykov AA. Cooperativity in catalysis by canonical family II pyrophosphatases. Biochem Biophys Res Commun 2019; 517:266-271. [DOI: 10.1016/j.bbrc.2019.07.056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 07/17/2019] [Indexed: 10/26/2022]
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Baykov AA, Anashkin VA, Salminen A, Lahti R. Inorganic pyrophosphatases of Family II-two decades after their discovery. FEBS Lett 2017; 591:3225-3234. [PMID: 28986979 DOI: 10.1002/1873-3468.12877] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 10/04/2017] [Accepted: 10/04/2017] [Indexed: 12/22/2022]
Abstract
Inorganic pyrophosphatases (PPases) convert pyrophosphate (PPi ) to phosphate and are present in all cell types. Soluble PPases belong to three nonhomologous families, of which Family II is found in approximately a quarter of prokaryotic organisms, often pathogenic ones. Each subunit of dimeric canonical Family II PPases is formed by two domains connected by a flexible linker, with the active site located between the domains. These enzymes require both magnesium and a transition metal ion (manganese or cobalt) for maximal activity and are the most active (kcat ≈ 104 s-1 ) among all PPase types. Catalysis by Family II PPases requires four metal ions per substrate molecule, three of which form a unique trimetal center that coordinates the nucleophilic water and converts it to a reactive hydroxide ion. A quarter of Family II PPases contain an autoinhibitory regulatory insert formed by two cystathionine β-synthase (CBS) domains and one DRTGG domain. Adenine nucleotide binding either activates or inhibits the CBS domain-containing PPases, thereby tuning their activity and, hence, PPi levels, in response to changes in cell energy status (ATP/ADP ratio).
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Affiliation(s)
- Alexander A Baykov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Russia
| | - Viktor A Anashkin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Russia
| | - Anu Salminen
- Department of Biochemistry, University of Turku, Finland
| | - Reijo Lahti
- Department of Biochemistry, University of Turku, Finland
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An asparagine residue mediates intramolecular communication in nucleotide-regulated pyrophosphatase. Biochem J 2016; 473:2097-107. [PMID: 27208172 DOI: 10.1042/bcj20160293] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 05/16/2016] [Indexed: 01/01/2023]
Abstract
Many prokaryotic soluble PPases (pyrophosphatases) contain a pair of regulatory adenine nucleotide-binding CBS (cystathionine β-synthase) domains that act as 'internal inhibitors' whose effect is modulated by nucleotide binding. Although such regulatory domains are found in important enzymes and transporters, the underlying regulatory mechanism has only begun to come into focus. We reported previously that CBS domains bind nucleotides co-operatively and induce positive kinetic co-operativity (non-Michaelian behaviour) in CBS-PPases (CBS domain-containing PPases). In the present study, we demonstrate that a homodimeric ehPPase (Ethanoligenens harbinense PPase) containing an inherent mutation in an otherwise conserved asparagine residue in a loop near the active site exhibits non-co-operative hydrolysis kinetics. A similar N312S substitution in 'co-operative' dhPPase (Desulfitobacterium hafniense PPase) abolished kinetic co-operativity while causing only minor effects on nucleotide-binding affinity and co-operativity. However, the substitution reversed the effect of diadenosine tetraphosphate, abolishing kinetic co-operativity in wild-type dhPPase, but restoring it in the variant dhPPase. A reverse serine-to-asparagine replacement restored kinetic co-operativity in ehPPase. Molecular dynamics simulations revealed that the asparagine substitution resulted in a change in the hydrogen-bonding pattern around the asparagine residue and the subunit interface, allowing greater flexibility at the subunit interface without a marked effect on the overall structure. These findings identify this asparagine residue as lying at the 'crossroads' of information paths connecting catalytic and regulatory domains within a subunit and catalytic sites between subunits.
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Tang Q, Luo Y, Zheng C, Yin K, Ali MK, Li X, He J. Functional Analysis of a c-di-AMP-specific Phosphodiesterase MsPDE from Mycobacterium smegmatis. Int J Biol Sci 2015; 11:813-24. [PMID: 26078723 PMCID: PMC4466462 DOI: 10.7150/ijbs.11797] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 05/04/2015] [Indexed: 12/21/2022] Open
Abstract
Cyclic di‑AMP (c-di-AMP) is a second signaling molecule involved in the regulation of bacterial physiological processes and interaction between pathogen and host. However, the regulatory network mediated by c-di-AMP in Mycobacterium remains obscure. In M. smegmatis, a diadenylate cyclase (DAC) was reported recently, but there is still no investigation on c-di-AMP phosphodiesterase (PDE). Here, we provide a systematic study on signaling mechanism of c-di-AMP PDE in M. smegmatis. Based on our enzymatic analysis, MsPDE (MSMEG_2630), which contained a DHH-DHHA1 domain, displayed a 200-fold higher hydrolytic efficiency (kcat/Km) to c-di-AMP than to c-di-GMP. MsPDE was capable of converting c-di-AMP to pApA and AMP, and hydrolyzing pApA to AMP. Site-directed mutations in DHH and DHHA1 revealed that DHH domain was critical for the phosphodiesterase activity. To explore the regulatory role of c-di-AMP in vivo, we constructed the mspde mutant (Δmspde) and found that deficiency of MsPDE significantly enhanced intracellular C12-C20 fatty acid accumulation. Deficiency of DAC in many bacteria results in cell death. However, we acquired the M. smegmatis strain with DAC gene disrupted (ΔmsdisA) by homologous recombination approach. Deletion of msdisA reduced bacterial C12-C20 fatty acids production but scarcely affected bacterial survival. We also provided evidences that superfluous c-di-AMP in M. smegmatis could lead to abnormal colonial morphology. Collectively, our results indicate that MsPDE is a functional c-di-AMP-specific phosphodiesterase both in vitro and in vivo. Our study also expands the regulatory network mediated by c-di-AMP in M. smegmatis.
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Affiliation(s)
- Qing Tang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Yunchao Luo
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Cao Zheng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Kang Yin
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Maria Kanwal Ali
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Xinfeng Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Jin He
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
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Identification and characterization of mutations conferring resistance to D-amino acids in Bacillus subtilis. J Bacteriol 2015; 197:1632-9. [PMID: 25733611 DOI: 10.1128/jb.00009-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 02/19/2015] [Indexed: 02/02/2023] Open
Abstract
UNLABELLED Bacteria produce d-amino acids for incorporation into the peptidoglycan and certain nonribosomally produced peptides. However, D-amino acids are toxic if mischarged on tRNAs or misincorporated into protein. Common strains of the Gram-positive bacterium Bacillus subtilis are particularly sensitive to the growth-inhibitory effects of D-tyrosine due to the absence of D-aminoacyl-tRNA deacylase, an enzyme that prevents misincorporation of D-tyrosine and other D-amino acids into nascent proteins. We isolated spontaneous mutants of B. subtilis that survive in the presence of a mixture of D-leucine, D-methionine, D-tryptophan, and D-tyrosine. Whole-genome sequencing revealed that these strains harbored mutations affecting tRNA(Tyr) charging. Three of the most potent mutations enhanced the expression of the gene (tyrS) for tyrosyl-tRNA synthetase. In particular, resistance was conferred by mutations that destabilized the terminator hairpin of the tyrS riboswitch, as well as by a mutation that transformed a tRNA(Phe) into a tyrS riboswitch ligand. The most potent mutation, a substitution near the tyrosine recognition site of tyrosyl-tRNA synthetase, improved enzyme stereoselectivity. We conclude that these mutations promote the proper charging of tRNA(Tyr), thus facilitating the exclusion of D-tyrosine from protein biosynthesis in cells that lack D-aminoacyl-tRNA deacylase. IMPORTANCE Proteins are composed of L-amino acids. Mischarging of tRNAs with D-amino acids or the misincorporation of D-amino acids into proteins causes toxicity. This work reports on mutations that confer resistance to D-amino acids and their mechanisms of action.
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Gajadeera CS, Zhang X, Wei Y, Tsodikov OV. Structure of inorganic pyrophosphatase from Staphylococcus aureus reveals conformational flexibility of the active site. J Struct Biol 2015; 189:81-6. [PMID: 25576794 DOI: 10.1016/j.jsb.2014.12.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 12/15/2014] [Accepted: 12/16/2014] [Indexed: 10/24/2022]
Abstract
Cytoplasmic inorganic pyrophosphatase (PPiase) is an enzyme essential for survival of organisms, from bacteria to human. PPiases are divided into two structurally distinct families: family I PPiases are Mg(2+)-dependent and present in most archaea, eukaryotes and prokaryotes, whereas the relatively less understood family II PPiases are Mn(2+)-dependent and present only in some archaea, bacteria and primitive eukaryotes. Staphylococcus aureus (SA), a dangerous pathogen and a frequent cause of hospital infections, contains a family II PPiase (PpaC), which is an attractive potential target for development of novel antibacterial agents. We determined a crystal structure of SA PpaC in complex with catalytic Mn(2+) at 2.1Å resolution. The active site contains two catalytic Mn(2+) binding sites, each half-occupied, reconciling the previously observed 1:1 Mn(2+):enzyme stoichiometry with the presence of two divalent metal ion sites in the apo-enzyme. Unexpectedly, despite the absence of the substrate or products in the active site, the two domains of SA PpaC form a closed active site, a conformation observed in structures of other family II PPiases only in complex with substrate or product mimics. A region spanning residues 295-298, which contains a conserved substrate binding RKK motif, is flipped out of the active site, an unprecedented conformation for a PPiase. Because the mutant of Arg295 to an alanine is devoid of activity, this loop likely undergoes an induced-fit conformational change upon substrate binding and product dissociation. This closed conformation of SA PPiase may serve as an attractive target for rational design of inhibitors of this enzyme.
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Affiliation(s)
- Chathurada S Gajadeera
- Department of Pharmaceutical Sciences, University of Kentucky, College of Pharmacy, 789 S. Limestone St., Lexington, KY 40536, United States
| | - Xinyi Zhang
- Department of Chemistry, University of Kentucky, 505 Rose St., Lexington, KY 40506, United States
| | - Yinan Wei
- Department of Chemistry, University of Kentucky, 505 Rose St., Lexington, KY 40506, United States.
| | - Oleg V Tsodikov
- Department of Pharmaceutical Sciences, University of Kentucky, College of Pharmacy, 789 S. Limestone St., Lexington, KY 40536, United States.
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Identification and characterization of an ecto-pyrophosphatase activity in intact epimastigotes of Trypanosoma rangeli. PLoS One 2014; 9:e106852. [PMID: 25203926 PMCID: PMC4159237 DOI: 10.1371/journal.pone.0106852] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Accepted: 08/09/2014] [Indexed: 02/06/2023] Open
Abstract
In this study, we performed the molecular and biochemical characterization of an ecto-enzyme present in Trypanosoma rangeli that is involved with the hydrolysis of extracellular inorganic pyrophosphate. PCR analysis identified a putative proton-pyrophosphatase (H+-PPase) in the epimastigote forms of T. rangeli. This protein was recognized with Western blot and flow cytometry analysis using an antibody against the H+-PPase of Arabidopsis thaliana. Immunofluorescence microscopy confirmed that this protein is located in the plasma membrane of T. rangeli. Biochemical assays revealed that the optimum pH for the ecto-PPase activity was 7.5, as previously demonstrated for other organisms. Sodium fluoride (NaF) and aminomethylenediphosphonate (AMDP) were able to inhibit approximately 75% and 90% of the ecto-PPase activity, respectively. This ecto-PPase activity was stimulated in a dose-dependent manner by MgCl2. In the presence of MgCl2, this activity was inhibited by millimolar concentrations of CaCl2. The ecto-PPase activity of T. rangeli decreased with increasing cell proliferation in vitro, thereby suggesting a role for this enzyme in the acquisition of inorganic phosphate (Pi). Moreover, this activity was modulated by the extracellular concentration of Pi and increased approximately two-fold when the cells were maintained in culture medium depleted of Pi. All of these results confirmed the occurrence of an ecto-PPase located in the plasma membrane of T. rangeli that possibly plays an important role in phosphate metabolism of this protozoan.
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Abstract
DNA replication is one of the most ancient of cellular processes and functional similarities among its molecular machinery are apparent across all cellular life. Cdc45 is one of the essential components of the eukaryotic replication fork and is required for the initiation and elongation of DNA replication, but its molecular function is currently unknown. In order to trace its evolutionary history and to identify functional domains, we embarked on a computational sequence analysis of the Cdc45 protein family. Our findings reveal eukaryotic Cdc45 and prokaryotic RecJ to possess a common ancestry and Cdc45 to contain a catalytic site within a predicted exonuclease domain. The likely orthology between Cdc45 and RecJ reveals new lines of enquiry into DNA replication mechanisms in eukaryotes.
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Affiliation(s)
- Luis Sanchez-Pulido
- Department of Physiology, Anatomy and Genetics, MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK.
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Ryan KC, Johnson OE, Cabelli DE, Brunold TC, Maroney MJ. Nickel superoxide dismutase: structural and functional roles of Cys2 and Cys6. J Biol Inorg Chem 2010; 15:795-807. [PMID: 20333421 PMCID: PMC3010328 DOI: 10.1007/s00775-010-0645-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Accepted: 02/11/2010] [Indexed: 11/28/2022]
Abstract
Nickel superoxide dismutase (NiSOD) is unique among the family of superoxide dismutase enzymes in that it coordinates Cys residues (Cys2 and Cys6) to the redox-active metal center and exhibits a hexameric quaternary structure. To assess the role of the Cys residues with respect to the activity of NiSOD, mutations of Cys2 and Cys6 to Ser (C2S-NiSOD, C6S-NiSOD, and C2S/C6S-NiSOD) were carried out. The resulting mutants do not catalyze the disproportionation of superoxide, but retain the hexameric structure found for wild-type NiSOD and bind Ni(II) ions in a 1:1 stoichiometry. X-ray absorption spectroscopic studies of the Cys mutants revealed that the nickel active-site structure for each mutant resembles that of C2S/C6S-NiSOD and demonstrate that mutation of either Cys2 or Cys6 inhibits coordination of the remaining Cys residue. Mutation of one or both Cys residue(s) in NiSOD induces the conversion of the low-spin Ni(II) site in the native enzyme to a high-spin Ni(II) center in the mutants. This result indicates that coordination of both Cys residues is required to generate the native low-spin configurations and maintain catalytic activity. Analysis of the quaternary structure of the Cys mutants by differential scanning calorimetry, mass spectrometry, and size-exclusion chromatography revealed that the Cys ligands, particularly Cys2, are also important for stabilizing the hexameric quaternary structure of the native enzyme.
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Affiliation(s)
- Kelly C. Ryan
- Department of Chemistry, University of Massachusetts at Amherst, 104 Lederle Graduate Research Tower A, 710 North Pleasant Street, Amherst, MA 01003, Phone: 413-545-4876, Fax: 413-545-4490
| | - Olivia E. Johnson
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706
| | - Diane E. Cabelli
- Department of Chemistry, Building 555A Brookhaven National Laboratory, P.O. Box 5000, Upton, NY 11973
| | - Thomas C. Brunold
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706
| | - Michael J. Maroney
- Department of Chemistry, University of Massachusetts at Amherst, 104 Lederle Graduate Research Tower A, 710 North Pleasant Street, Amherst, MA 01003, Phone: 413-545-4876, Fax: 413-545-4490
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Catalysis by isolated beta-subunits of the ATP Synthase/ATPase from Thermophilic bacillus PS3. Hydrolysis of pyrophosphate. J Bioenerg Biomembr 2009; 40:561-8. [PMID: 19139978 DOI: 10.1007/s10863-008-9192-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Accepted: 12/12/2008] [Indexed: 10/21/2022]
Abstract
Although the capacity of isolated beta-subunits of the ATP synthase/ATPase to perform catalysis has been extensively studied, the results have not conclusively shown that the subunits are catalytically active. Since soluble F(1) of mitochondrial H(+)-ATPase can bind inorganic pyrophosphate (PP(i)) and synthesize PP(i) from medium phosphate, we examined if purified His-tagged beta-subunits from Thermophilic bacillus PS3 can hydrolyze PP(i). The difference spectra in the near UV CD of beta-subunits with and without PP(i) show that PP(i) binds to the subunits. Other studies show that beta-subunits hydrolyze [(32)P] PP(i) through a Mg(2+)-dependent process with an optimal pH of 8.3. Free Mg(2+) is required for maximal hydrolytic rates. The Km for PP(i) is 75 microM and the Vmax is 800 pmol/min/mg. ATP is a weak inhibitor of the reaction, it diminishes the Vmax and increases the Km for PP(i). Thus, isolated beta-subunits are catalytically competent with PP(i) as substrate; apparently, the assembly of beta-subunits into the ATPase complex changes substrate specificity, and leads to an increase in catalytic rates.
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Rodina EV, Vainonen LP, Vorobyeva NN, Kurilova SA, Sitnik TS, Nazarova TI. Metal cofactors play a dual role in Mycobacterium tuberculosis inorganic pyrophosphatase. BIOCHEMISTRY (MOSCOW) 2008; 73:897-905. [DOI: 10.1134/s0006297908080075] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Tammenkoski M, Koivula K, Cusanelli E, Zollo M, Steegborn C, Baykov AA, Lahti R. Human Metastasis Regulator Protein H-Prune is a Short-Chain Exopolyphosphatase. Biochemistry 2008; 47:9707-13. [DOI: 10.1021/bi8010847] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marko Tammenkoski
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland, Department of Biochemistry and Biotechnological Medicine, Via Pansini 5, University Federico II of Naples, Italy, c/o CEINGE, Centro di Ingegneria Genetica e Biotecnologie Avanzate, Naples, Italy, Department of Physiological Chemistry, Ruhr-University Bochum, 44801 Bochum, Germany, and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
| | - Katja Koivula
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland, Department of Biochemistry and Biotechnological Medicine, Via Pansini 5, University Federico II of Naples, Italy, c/o CEINGE, Centro di Ingegneria Genetica e Biotecnologie Avanzate, Naples, Italy, Department of Physiological Chemistry, Ruhr-University Bochum, 44801 Bochum, Germany, and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
| | - Emilio Cusanelli
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland, Department of Biochemistry and Biotechnological Medicine, Via Pansini 5, University Federico II of Naples, Italy, c/o CEINGE, Centro di Ingegneria Genetica e Biotecnologie Avanzate, Naples, Italy, Department of Physiological Chemistry, Ruhr-University Bochum, 44801 Bochum, Germany, and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
| | - Massimo Zollo
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland, Department of Biochemistry and Biotechnological Medicine, Via Pansini 5, University Federico II of Naples, Italy, c/o CEINGE, Centro di Ingegneria Genetica e Biotecnologie Avanzate, Naples, Italy, Department of Physiological Chemistry, Ruhr-University Bochum, 44801 Bochum, Germany, and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
| | - Clemens Steegborn
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland, Department of Biochemistry and Biotechnological Medicine, Via Pansini 5, University Federico II of Naples, Italy, c/o CEINGE, Centro di Ingegneria Genetica e Biotecnologie Avanzate, Naples, Italy, Department of Physiological Chemistry, Ruhr-University Bochum, 44801 Bochum, Germany, and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
| | - Alexander A. Baykov
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland, Department of Biochemistry and Biotechnological Medicine, Via Pansini 5, University Federico II of Naples, Italy, c/o CEINGE, Centro di Ingegneria Genetica e Biotecnologie Avanzate, Naples, Italy, Department of Physiological Chemistry, Ruhr-University Bochum, 44801 Bochum, Germany, and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
| | - Reijo Lahti
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland, Department of Biochemistry and Biotechnological Medicine, Via Pansini 5, University Federico II of Naples, Italy, c/o CEINGE, Centro di Ingegneria Genetica e Biotecnologie Avanzate, Naples, Italy, Department of Physiological Chemistry, Ruhr-University Bochum, 44801 Bochum, Germany, and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
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14
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Tammenkoski M, Moiseev V, Lahti M, Ugochukwu E, Brondijk THC, White SA, Lahti R, Baykov AA. Kinetic and mutational analyses of the major cytosolic exopolyphosphatase from Saccharomyces cerevisiae. J Biol Chem 2007; 282:9302-9311. [PMID: 17215253 DOI: 10.1074/jbc.m609423200] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Yeast exopolyphosphatase (scPPX) processively splits off the terminal phosphate group from linear polyphosphates longer than pyrophosphate. scPPX belongs to the DHH phosphoesterase superfamily and is evolutionarily close to the well characterized family II pyrophosphatase (PPase). Here, we used steady-state kinetic and binding measurements to elucidate the metal cofactor requirement for scPPX catalysis over the pH range 4.2-9.5. A single tight binding site for Mg(2+) (K(d) of 24 microm) was detected by equilibrium dialysis. Steady-state kinetic analysis of tripolyphosphate hydrolysis revealed a second site that binds Mg(2+) in the millimolar range and modulates substrate binding. This step requires two protonated and two deprotonated enzyme groups with pK(a) values of 5.0-5.3 and 7.6-8.2, respectively. The catalytic step requiring two deprotonated groups (pK(a) of 4.6 and 5.6) is modulated by ionization of a third group (pK(a) of 8.7). Conservative mutations of Asp(127), His(148), His(149) (conserved in scPPX and PPase), and Asn(35) (His in PPase) reduced activity by a factor of 600-5000. N35H and D127E substitutions reduced the Mg(2+) affinity of the tight binding site by 25-60-fold. Contrary to expectations, the N35H variant was unable to hydrolyze pyrophosphate, but markedly altered metal cofactor specificity, displaying higher catalytic activity with Co(2+) bound to the weak binding site versus the Mg(2+)- or Mn(2+)-bound enzyme. These results provide an initial step toward understanding the dynamics of scPPX catalysis and reveal significant functional differences between structurally similar scPPX and family II PPase.
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Affiliation(s)
- Marko Tammenkoski
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland
| | - ViktorM Moiseev
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
| | - Matti Lahti
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland
| | - Emilie Ugochukwu
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - T Harma C Brondijk
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Scott A White
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Reijo Lahti
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland.
| | - Alexander A Baykov
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia.
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15
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Fabrichniy IP, Lehtiö L, Tammenkoski M, Zyryanov AB, Oksanen E, Baykov AA, Lahti R, Goldman A. A Trimetal Site and Substrate Distortion in a Family II Inorganic Pyrophosphatase. J Biol Chem 2007; 282:1422-31. [PMID: 17095506 DOI: 10.1074/jbc.m513161200] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We report the first crystal structures of a family II pyrophosphatase complexed with a substrate analogue, imidodiphosphate (PNP). These provide new insights into the catalytic reaction mechanism of this enzyme family. We were able to capture the substrate complex both by fluoride inhibition and by site-directed mutagenesis providing complementary snapshots of the Michaelis complex. Structures of both the fluoride-inhibited wild type and the H98Q variant of the PNP-Bacillus subtilis pyrophosphatase complex show a unique trinuclear metal center. Each metal ion coordinates a terminal oxygen on the electrophilic phosphate and a lone pair on the putative nucleophile, thus placing it in line with the scissile bond without any coordination by protein. The nucleophile moves further away from the electrophilic phosphorus site, to the opposite side of the trimetal plane, upon binding of substrate. In comparison with earlier product complexes, the side chain of Lys296 has swung in and so three positively charged side chains, His98, Lys205 and Lys296, now surround the bridging nitrogen in PNP. Finally, one of the active sites in the wild-type structure appears to show evidence of substrate distortion. Binding to the enzyme may thus strain the substrate and thus enhance the catalytic rate.
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Affiliation(s)
- Igor P Fabrichniy
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Biocenter 3, P. O. Box 65, FIN-00014 Helsinki, Finland
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Tammenkoski M, Benini S, Magretova NN, Baykov AA, Lahti R. An Unusual, His-dependent Family I Pyrophosphatase from Mycobacterium tuberculosis. J Biol Chem 2005; 280:41819-26. [PMID: 16239227 DOI: 10.1074/jbc.m509489200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Soluble inorganic pyrophosphatases (PPases) comprise two evolutionarily unrelated families (I and II). These two families have different specificities for metal cofactors, which is thought to be because of the fact that family II PPases have three active site histidines, whereas family I PPases have none. Here, we report the structural and functional characterization of a unique family I PPase from Mycobacterium tuberculosis (mtPPase) that has two His residues (His21 and His86) in the active site. The 1.3-A three-dimensional structure of mtPPase shows that His86 directly interacts with bound sulfate, which mimics the product phosphate. Otherwise, mtPPase is structurally very similar to the well studied family I hexameric PPase from Escherichia coli, although mtPPase lacks the intersubunit metal binding site found in E. coli PPase. The cofactor specificity of mtPPase resembles that of E. coli PPase in that it has high activity in the presence of Mg2+, but it differs from the E. coli enzyme and family II PPases because it has much lower activity in the presence of Mn2+ or Zn2+. Replacements of His21 and His86 in mtPPase with the residues found in the corresponding positions of E. coli PPase had either no effect on the Mg2+- and Mn2+-supported reactions (H86K) or reduced Mg2+-supported activity (H21K). However, both replacements markedly increased the Zn2+-supported activity of mtPPase (up to 11-fold). In the double mutant, Zn2+ was a 2.5-fold better cofactor than Mg2+. These results show that the His residues in mtPPase are not essential for catalysis, although they determine cofactor specificity.
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Affiliation(s)
- Marko Tammenkoski
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland
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Espiau B, Lemercier G, Ambit A, Bringaud F, Merlin G, Baltz T, Bakalara N. A soluble pyrophosphatase, a key enzyme for polyphosphate metabolism in Leishmania. J Biol Chem 2005; 281:1516-23. [PMID: 16291745 DOI: 10.1074/jbc.m506947200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We report the functional characterization in Leishmania amazonensis of a soluble pyrophosphatase (LaVSP1) that localizes in acidocalcisomes, a vesicular acidic compartment. LaVSP1 is preferentially expressed in metacyclic forms. Experiments with dominant negative mutants show the requirement of LaVSP1 functional expression for metacyclogenesis and virulence in mice. Depending on the pH and the cofactors Mg2+ or Zn2+, both present in acidocalcisomes, LaVSP1 hydrolyzes either inorganic pyrophosphate (Km = 92 microM, kcat = 125 s(-1)), tripolyphosphate (Km = 1153 microM, kcat = 131 s(-1)), or polyphosphate of 28 residues (Km = 123 microM, kcat = 8 s(-1)). Predicted structural analysis suggests that the structural orientation of the residue Lys78 in LaVSP1 accounts for the observed increase in Km compared with the yeast pyrophosphatase and for the ability of trypanosomatid VSP1 enzymes to hydrolyze polyphosphate. These results make the VSP1 enzyme an attractive drug target against trypanosomatid parasites.
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Affiliation(s)
- Benoît Espiau
- Laboratoire de Génomique Fonctionnelle des Trypanosomatides, Université Victor Segalen Bordeaux 2, UMR-CNRS 5162, 146 rue Léo Saignat, 33076 Bordeaux, France
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